K2CO3-mediated annulation of 1,3-acetonedicarboxylates with 2-fluoro-1-nitroarenes: synthesis of indoles.

The K2CO3-mediated one-pot reaction of 1,3-acetonedicarboxylates with 2 equiv. of substituted 2-fluoro-1-nitrobenzenes has been developed to synthesize various 2,3-dicarboxylate indoles via a tandem annulation pathway. In the effective reaction, one carbon-carbon double bond, one carbon-carbon single bond and one carbon-nitrogen single bond are formed under open-vessel conditions. DFT calculations are used to rationalize the plausible mechanisms.

DFT study on the catalytic decomposition of hydrogen peroxide by iron complexes of nitrilotriacetate.

The Fenton system in the presence of nitrilotriacetate (NTA) ligand is studied by DFT approach. The calculations show that complexation of Fe(II) with NTA significantly facilitates the H2 O2 activation. The ferric-hydroperoxo intermediate NTAFe(III)OOH predominantly decays via the disproportionation into NTAFe(II)OH2 and NTAFe(IV)O involving the formation of a µ-1,2-hydroperoxo-bridged biferric intermediate. In this mechanism, the bridged hydroperoxo is reduced by hydroperoxo ligand rather than by Fe(III). On the one hand, the NTAFe(III)OOH is sluggish to undergo hydrogen abstraction; on the other hand, it is a good nucleophile that may perform aldehyde deformylation. The present calculations suggest that both ˙OH and Fe(IV)O are generated in the NTA-assisted Fenton system. However, the polycarboxylate ligand provides a favorable environment for H2 O2 to accumulate around iron ion through hydrogen bonding. This promotes the quenching of Fe(IV)O by H2 O2 , rationalizing why the Fe(IV)O species is hardly detected in the NTA-assisted Fenton system.

Ring-Opening Polymerization of ε-Caprolactone by Using Aluminum Complexes Bearing Aryl Thioether Phenolates: Labile Thioether Chelation.

In this study, aluminum complexes bearing ferrocene-based and arylthiomethylphenolate ligands were synthesized, and their catalytic activity for ε-caprolactone (CL) polymerization was investigated. The catalytic activity of the reduced form of Al complexes was higher than that of the oxidized form. The CL polymerization rate of the reduced form fcO2AlMe (75 min, conversion = 100%) was higher than that of the oxidized form fcoxO2AlMe (4320 min, conversion = 45%), and the CL polymerization rate of fc(OAlMe2)2 (40 min, conversion = 100%) was higher than that of fcox(OAlMe2)2 (60 min, conversion = 97%). Electron deficiency substituents on phenolate decreased the catalytic activity of Al complexes bearing arylthiomethylphenolate ligands. Density functional theory calculations revealed that thioether coordination stabilized the transition state (TS1) and that the oxidized form fcox(OAlMe2)2 exhibited weaker thioether coordination and higher activation energy in TS1 compared with those of the reduced form fcO2AlMe. In addition, our study determined that the thioether group is a suitable chelating group for Al catalysts in CL polymerization due to its labile nature.

Near-IR Charge-Transfer Emission at 77 K and Density Functional Theory Modeling of Ruthenium(II)-Dipyrrinato Chromophores: High Phosphorescence Efficiency of the Emitting State Related to Spin-Orbit Coupling Mediation of Intensity from Numerous Low-Energy Singlet Excited States.

Efficient charge-transfer (CT) phosphorescence in the near-IR (NIR) spectral region is reported for four substituted Ru-(R-dipyrrinato) complexes, [Ru(bpy)2(R-dipy)](PF6), where bpy is 2,2'-bipyridine and the substituent R is phenyl (ph), 2,4,6-trimethylphenyl, 4-carboxyphenyl (HOOC-ph), or 4-pyridinyl. The experimentally determined phosphorescence efficiency, ιem(p) = kRAD(p)/(νem(p))3 (where kRAD(p) and νem(p) are the phosphorescence rate constant and the phosphorescence frequency, respectively), of the [Ru(bpy)2(R-dipy)]+ complexes was approximately double that of [Ru(bpy)(Am)4]2+ complexes (Am = ammine ligand) in the NIR region. Density functional theory (DFT) modeling indicated two strikingly different electronic configurations of the triplet emitting state (Te) in the two types of complexes. The Te of [Ru(bpy)2(R-dipy)]+ complexes shows a CT-type corresponding to the metal-to-ligand charge transfer (MLCT)-(Ru-(R-dipy)) and the ππ*-(R-dipy) moiety configurations, and the Te state in the [Ru(bpy)(Am)4]2+ complexes corresponds to an approximately MLCT excited state consisting of mostly MLCT-(Ru-bpy) with a minimal ππ*(bpy) contribution. DFT modeling also indicated that the low-energy singlet excited states in the Te geometry (Sn(T)) of the [Ru(bpy)2(ph-dipy)]+ complex consist of numerous CT-Sn(T)-type states of the Ru-dipy and Ru-bpy moieties, whereas the [Ru(bpy)(Am)4]2+ ions show quite simple MLCT-Sn(T)-type states of the Ru-bpy moiety. Based on experimental observations, DFT modeling, and the plain spin-orbit coupling (SOC) principle, we conclude that the remarkably high ιem(p) amplitudes of the [Ru(bpy)2(R-dipy)]+ complexes relative to those of [Ru(bpy)(Am)4]2+ complexes can be attributed to the relatively substantial contribution of intrinsic SOC-mediated intensity stealing from the numerous low-energy CT-type Sn(T) states.

Synergistic Catalysis by Brønsted Acid/Carbodicarbene Mimicking Frustrated Lewis Pair-Like Reactivity.

Carbodicarbene (CDC), unique carbenic entities bearing two lone pairs of electrons are well-known for their strong Lewis basicity. We demonstrate herein, upon introducing a weak Brønsted acid benzyl alcohol (BnOH) as a co-modulator, CDC is remolded into a Frustrated Lewis Pair (FLP)-like reactivity. DFT calculation and experimental evidence show BnOH loosely interacting with the binding pocket of CDC via H-bonding and π-π stacking. Four distinct reactions in nature were deployed to demonstrate the viability of proof-of-concept as synergistic FLP/Modulator (CDC/BnOH), demonstrating enhanced catalytic reactivity in cyclotrimerization of isocyanate, polymerization process for L-lactide (LA), methyl methacrylate (MMA) and dehydrosilylation of alcohols. Importantly, the catalytic reactivity of carbodicarbene is uniquely distinct from conventional NHC which relies on only single chemical feature of nucleophilicity. This finding also provides a new spin in diversifying FLP reactivity with co-modulator or co-catalyst.

CuBr2-Mediated One-Pot Synthesis of Sulfonyl 9-Fluorenylidenes.

In this article, a high-yield method for the synthesis of sulfonyl 9-fluorenylidenes is described, which consists of a one-pot straightforward three-step synthetic route, including (i) CuBr2-mediated α-bromination of o-arylacetophenone, (ii) sequential nucleophilic substitution of the resulting α-bromo o-arylacetophenone with sodium sulfinate (RSO2Na), and (iii) the CuBr2-mediated intramolecular Friedel-Crafts cyclizative dehydration. A plausible mechanism is proposed and discussed. This protocol provides a highly effective regio- and stereoselective annulation via the formation of one carbon-carbon (C-C) bond and one carbon-sulfur (C-S) bond.

Synthesis of 2-Sulfonyl Indenes and Indanes.

In this paper, we developed facile and high-yield synthetic routes for the preparation of 2-sulfonyl indenes and indanes, including: (i) Amberlyst-15-promoted Knoevenagel reaction of ß-ketosulfones and arylaldehydes in refluxing toluene; (ii) Grignard reagent (R'MgBr) or reducing reagent (NaBH4) promoted regio- and/or stereocontrolled 1,4-addition or 1,4-/1,2-reduction of the resulting sulfonyl chalcones in THF or MeOH/THF at 25 °C; and then (iii) Amberlyst-15 mediated intramolecular Friedel-Crafts annulation of the corresponding ß-ketosulfones or ß-hydroxysulfones in toluene at reflux. This present method describes a highly efficient (3 + 2) annulation via the formation of two carbon-carbon (C-C) bonds. The DFT calculations were utilized to rationalize the regioselectivity of the addition reaction.

Construction of Sulfonyl Dihydrobenzo[c]xanthen-7-ones Core via NH4OAc/PdCl2/CuCl2-Mediated Double Cyclocondensation of α-Sulfonyl o-Hydroxyacetophenones with 2-Allylbenzaldehydes.

NH4OAc/PdCl2/CuCl2 mediated domino double cyclocondensation of α-sulfonyl o-hydroxyacetophenones and 2-allylbenzaldehydes provides tetracyclic sulfonyl dihydrobenzo[c]xanthen-7-one core with good to excellent yields in MeOH. The intermediates contain a 3-sulfonyl flavanone motif. Only water is generated as a byproduct. The use of various catalysts and reaction conditions is studied for the facile-operational conversion.

Low-Temperature Spectra and Density Functional Theory Modeling of Ru(II)-Bipyridine Complexes with Cyclometalated Ancillary Ligands: The Excited State Spin-Orbit Coupling Origin of Variations in Emission Efficiencies.

The 77 K emission spectra of cyclometalated ruthenium(II)-2,2'-bipyridine (CM-Ru-bpy) chromophores are very similar to those of related Ru-bpy complexes with am(m)ine or diimmine ancillary ligands, and density functional theory (DFT) modeling confirms that the lowest energy triplet metal to ligand charge transfer (3MLCT) excited states of CM-Ru-bpy and related Ru-bpy complexes have very similar electronic configurations. However, the phosphorescence decay efficiencies of CM-Ru-bpy excited states are about twice those of the conventional Ru-bpy analogues. In contrast to the similar 3MLCT excited state electronic configurations of the two classes of complexes, the CM-Ru-bpy chromophores have much broader visible region MLCT absorptions resulting from several overlapping transitions, even at 87 K. The emitting excited-state emission efficiencies depend on spin-orbit coupling (SOC) mediated intensity stealing from singlet excited states, and this work explores the relationship between the phosphorescence efficiency and visible region absorption spectra of Ru-bpy 3MLCT excited states in the weak SOC limit. The intrinsic 3MLCT emission efficiency, ιem, depends on mixing with singlet excited states whose RuIII-dπ-orbital angular momenta differ from that of the emitting state. DFT modeling of the 1MLCT excited-state electronic configurations that contribute significantly to the lowest energy absorption bands have RuIII-dπ orbitals that differ from those of their emitting 3MLCT excited states. This leads to a very close relationship between ιem and the lowest energy MLCT band absorptivities in Ru-bpy chromophores. Thus, the larger number of 1MLCT transitions that contribute to the lowest energy absorption bands accounts for the enhanced phosphorescence efficiency of Ru-bpy complexes with cyclometalated ancillary ligands.

Synthesis and Photophysical Characterization of 2,3-Dihydroquinolin-4-imines: New Fluorophores with Color-Tailored Emission.

In this study, a series of variously substituted 2,3-dihydroquinolin-4-imines (DQIs) were synthesized from N-substituted propargylanilines by copper(I)-catalyzed annulation. The approach adopted in this study under mild, effective conditions exhibited broad substrate tolerance, particularly for functional groups substituted on anilines. Most of the DQI derivatives synthesized under optimal conditions were obtained in good isolated yields of 63-88 %. 2,3-Dihydroquinolinimine thus obtained was easily converted to important structures like 2,3-dihydroquinolone and tetrahydrobenzodiazepin-5-one, confirming the importance of this strategy in constructing various heterocycles. Surprisingly, 2,3-dihydroquinolinimines thus obtained exhibited bright fluorescence with quantum yields up to 66 %. The density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations were performed for understanding the excited-state nature of DQI system. Accordingly, a tailored DQI derivative bearing methoxy group at C-6 position and acetoxy group at C-7 position was designed and synthesized to give emission at 559 nm with redshift compared to the 7-methoxy substituted DQI. A detailed study of DQI structures with their photophysical properties was performed with five control molecules and consequently demonstrated the uniqueness of the chemical structures of DQIs.

A computational study of the Fenton reaction in different pH ranges.

The reaction of iron(ii) and hydrogen peroxide, namely the Fenton reaction, is well-known for its strong oxidizing capability. While the Fenton reactions are ubiquitous and have wide applications in many areas, the detailed mechanism, especially the nature of the reactive intermediates responsible for oxidation, is not completely clear. In this work, the performances of various density functional theory (DFT) methods on the relative energies of key Fenton intermediates are evaluated. The DFT method selected from the benchmark study is then exploited to investigate the aqueous Fenton reactions in different pH conditions. The results show that at pH > 2.2, the major Fenton oxidants are high-valent oxoiron(iv) aquo complexes. However, depending on the pH conditions, these complexes can exist in three protonation states that display quite different oxidation reactivities. The oxidizing power of FeIV[double bond, length as m-dash]O is found to be principally determined by the total charge of the ligands and is less influenced by the axial ligand effect. Moreover, the calculations reveal that the presence of the hydronium ion can stabilize the intermediate of the hydroxyl radical and further inhibit oxoiron(iv) formation via proton transfer. The contribution of hydroxyl radicals could compete with the oxoiron(iv) species at pH below 2.2. In addition, high-level ab initio calculations question the existence of the iron(iv)-dihydroxo intermediate suggested in the literature. The implications of the computational results for the Fenton oxidation process, cytochrome P450, and catalyst design are discussed.

Catalytic polymerization of naphthalene by HF/BF3 super acid: an ab initio density functional theory study.

Mesophase pitch fabricated through polymerization of polycyclic aromatic hydrocarbons (PAHs) is highly aromatic and of high quality, and it can be used as a raw material to produce other carbon-based materials. Hydrofluoride/boron trifluoride (HF/BF3) is currently an efficient reagent to catalyze the PAH polymerization to produce mesophase pitch. In this study, density functional theory (DFT) calculations are performed to propose a mechanism for naphthalene catalytic polymerization using HF/BF3. The overall reaction mechanism can be conceptualized as having two stages: activation, followed by polymerization. During activation, HF/BF3 acts a proton donor to activate naphthalene, whose then-protonated form can promote the formation of a C-C bond with another naphthalene molecule via electrophilic addition. We also propose a catalyst recovery pathway, which can stabilize the intermediate products. In the polymerization stage, two types of pathways are proposed, those of chain elongation and intramolecular cyclization. According to the proposed catalytic mechanism in this study, the predicted mesophase product shows highly aliphatic hydrogens, which is consistent with the experimental results. We propose the full catalytic mechanism using DFT calculations. Our results provide a better understanding of how to develop novel and green catalysts, which can replace the HF/BF3 reagent in future applications.

Construction of Sulfonyl Oxabenzo[3.3.1]bicyclic Core via Cyclocondensation of ß-Ketosulfones and o-Formyl Allylbenzenes.

NH4OAc mediated domino Knoevenagel/Diels-Alder cyclocondensation of ß-ketosulfones 1 and o-formyl allylbenzenes 2 provides sulfonyl oxabenzo[3.3.1]bicyclic core 4 in a cosolvent of toluene and HOAc (v/v = 1/1) at reflux for 3 h. The intermediate 3 contains a chalcone motif. The uses of various ammonium salts and solvent systems are investigated for facile and efficient transformation. The plausible mechanisms have been proposed and the DFT calculations have been included.

Halogen-Mediated Cascade Cyclization Reaction of Aryldiynes to Indeno[1,2-c]chromene Derivatives.

The halogen-mediated cyclization reaction of aryldiynes to produce halogenated indeno[1,2-c]chromene derivatives is described. Treatment of aryldiynes 1 with one equivalent of iodine gave iodinated indeno[1,2-c]chromenes 3 in good chemical yields. When two equivalents of iodine were employed into the reaction mixture, dimer 9 was obtained as the major products. On the other hand, reaction of two equivalents of CuBr2 with compounds 1 gave the brominated indeno[1,2-c]chromenes 4. The DFT calculation of the iodine-mediated cyclization reactions for molecules containing methoxy, carboxy, amino, and sulfide substituents were carried out in order to understand how the substituent affects the cyclization pathway.

Reactivity Study of Unsymmetrical ß-Diketiminato Copper(I) Complexes: Effect of the Chelating Ring.

ß-Diketiminato copper(I) complexes play important roles in bioinspired catalytic chemistry and in applications to the materials industry. However, it has been observed that these complexes are very susceptible to disproportionation. Coordinating solvents or Lewis bases are typically used to prevent disproportionation and to block the coordination sites of the copper(I) center from further decomposition. Here, we incorporate this coordination protection directly into the molecule in order to increase the stability and reactivity of these complexes and to discover new copper(I) binding motifs. Here we describe the synthesis, structural characterization, and reactivity of a series of unsymmetrical N-aryl-N'-alkylpyridyl ß-diketiminato copper(I) complexes and discuss the structures and reactivity of these complexes with respect to the length of the pyridyl arm. All of the aforementioned unsymmetrical ß-diketiminato copper(I) complexes bind CO reversibly and are stable to disproportionation. The binding ability of CO and the rate of pyridyl ligand decoordination of these copper(I) complexes are directly related to the competition between the degree of puckering of the chelate system and the steric demands of the N-aryl substituent.

Improvement in Titanium Complexes Bearing Schiff Base Ligands in the Ring-Opening Polymerization of L-Lactide: A Dinuclear System with Hydrazine-Bridging Schiff Base Ligands.

A series of titanium (Ti) complexes bearing hydrazine-bridging Schiff base ligands were synthesized and investigated as catalysts for the ring-opening polymerization (ROP) of L-lactide (LA). Complexes with electron withdrawing or steric bulky groups reduced the catalytic activity. In addition, the steric bulky substituent on the imine groups reduced the space around the Ti atom and then reduced LA coordination with Ti atom, thereby reducing catalytic activity. All the dinuclear Ti complexes exhibited higher catalytic activity (approximately 10-60-fold) than mononuclear L(Cl-H)-TiOPr2 did. The strategy of bridging dinuclear Ti complexes with isopropoxide groups in the ROP of LA was successful, and adjusting the crowded heptacoordinated transition state by the bridging isopropoxide groups may be the key to our successful strategy.

Comparative Study of Aluminum Complexes Bearing N,O- and N,S-Schiff Base in Ring-Opening Polymerization of ε-Caprolactone and L-Lactide.

A series of Al complexes bearing Schiff base and thio-Schiff base ligands were synthesized, and their application for the ring-opening polymerization of ε-caprolactone (CL) and l-lactide (LA) was studied. It was found that steric effects of the ligands caused higher polymerization rate and most importantly the Al complexes with N,S-Schiff base showed significantly higher polymerization rate than Al complexes with N,O-Schiff base (5-12-fold for CL polymerization and 2-7-fold for LA polymerization). The reaction mechanism of CL polymerization was investigated by density functional theory (DFT). The calculations predicted a lower activation energy for a process involved with an Al complex bearing an N,S-Schiff base ligand (17.6 kcal/mol) than for that of an Al complex bearing an N,O-Schiff base ligand (19.0 kcal/mol), and this magnitude of activation energy reduction is comparable to the magnitude of rate enhancement observed in the experiment. The reduction of activation energy was attributed to the catalyst-substrate destabilization effect. Using a sulfur-containing ligand to decrease the activation energy in the ring-opening polymerization process may be a new strategy to design a new Al complex with high catalytic activity.

Effective and site-specific phosphoramidation reaction for universally labeling nucleic acids.

Here we report efficient and selective postsynthesis labeling strategies, based on an advanced phosphoramidation reaction, for nucleic acids of either synthetic or enzyme-catalyzed origin. The reactions provided phosphorimidazolide intermediates of DNA or RNA which, whether reacted in one pot (one-step) or purified (two-step), were directly or indirectly phosphoramidated with label molecules. The acquired fluorophore-labeled nucleic acids, prepared from the phosphoramidation reactions, demonstrated labeling efficacy by their F/N ratio values (number of fluorophores per molecule of nucleic acid) of 0.02-1.2 which are comparable or better than conventional postsynthesis fluorescent labeling methods for DNA and RNA. Yet, PCR and UV melting studies of the one-step phosphoramidation-prepared FITC-labeled DNA indicated that the reaction might facilitate nonspecific hybridization in nucleic acids. Intrinsic hybridization specificity of nucleic acids was, however, conserved in the two-step phosphoramidation reaction. The reaction of site-specific labeling nucleic acids at the 5'-end was supported by fluorescence quenching and UV melting studies of fluorophore-labeled DNA. The two-step phosphoramidation-based, effective, and site-specific labeling method has the potential to expedite critical research including visualization, quantification, structural determination, localization, and distribution of nucleic acids in vivo and in vitro.

Interaction of electrons with cisplatin and the subsequent effect on DNA damage: a density functional theory study.

Cisplatin, Pt(NH3)2Cl2, is a leading chemotherapeutic agent that has been widely used for various cancers. Recent experiments show that combining cisplatin and electron sources can dramatically enhance DNA damage and the cell-killing rate and, therefore, is a promising way to overcome the side effects and the resistance of cisplatin. However, the molecular mechanisms underlying this phenomenon are not clear yet. By using density functional theory calculations, we confirm that cisplatin can efficiently capture the prehydrated electrons and then undergo dissociation. The first electron attachment triggers a spontaneous departure of the chloride ion, forming a T-shaped [Pt(NH3)2Cl]˙ neutral radical, whereas the second electron attachment leads to a spontaneous departure of ammine, forming a linear [Pt(NH3)Cl](-) anion. We further recognize that the one-electron reduced product [Pt(NH3)2Cl]˙ is extremely harmful to DNA. It can abstract hydrogen atoms from the C-H bonds of the ribose moiety and the methyl group of thymine, which in turn leads to DNA strand breaks and cross-link lesions. The activation energies of these hydrogen abstraction reactions are relatively small compared to the hydrolysis of cisplatin, a prerequisite step in the normal mechanism of action of cisplatin. These results rationalize the improved cytotoxicity of cisplatin by supplying electrons. Although the biological effects of the two-electron reduced product [Pt(NH3)Cl](-) are not clear at this stage, our calculations indicate that it might be protonated by the surrounding water.

Unraveling the binding mechanisms of SARS-CoV-2 variants through molecular simulations.

The emergence of SARS-CoV-2 variants like Delta (AY.29) and Omicron (EG.5) poses continued challenges for vaccines and therapeutics. Mutations in the viral spike protein are key in altering infectivity and immune evasion. This study uses computational modeling to investigate the molecular binding mechanisms between spike protein variants and the ACE2 host receptor. Using the MARTNI force field, coarse-grained molecular dynamics (CGMD) simulations and nudged elastic band (NEB) calculations explore spike-ACE2 interactions for the wild type, Delta variant, and Omicron variant. The simulations reveal Omicron has the strongest binding affinity at -128.35 ± 10.91 kcal/mol, followed by Delta and wild type. Key mutations in Delta and Omicron, like Q493R and Q498R, optimize electrostatic contacts, enhancing ACE2 interactions. The wild-type spike has the highest transition state energy barrier at 17.87 kcal/mol, while Delta has the lowest barrier at 9.21 kcal/mol. Despite slightly higher dual barriers, Omicron's increased binding energy lowers its overall barrier to rapidly bind ACE2. These findings provide residue-level insights into mutation effects on SARS-CoV-2 infectivity. The computational modeling elucidates mechanisms underlying spike-ACE2 binding kinetics, aiding the development of vaccines and therapies targeting emerging viral strains.